I'm having some problems to understand the Cufflinks FPKMs... I use Cufflinks to obtain the FPKMs froma a ".sam" file obtained from the denovo assembly permormed wit MIRA3 of a transcriptome. Cufflinks give me us an output the files "Isoforms.fpkm_trasckin" and "genes.fpkm_tracking", in both files the FPKMs values are the same. However, I tried to apply the formula FPKM=10^9*numreads_of_the_fragment/(total_assembled_reads * length_of_the_fragment)) and the values are ttally different, with non apparent correlation...

Did you read the cufflinks paper? It's a lot more complicated than that... Not sure it's really possible to put it into a text box, even if I did claim to understand it. Supplementary methods section 3, lots of math.

Handling of multimapped reads. I believe that Cufflinks evenly divides a read between all places that it maps. For example, a read that is mapped to 4 locations is counted as .25 reads at each individual locus.

If any of your transcripts overlap (i.e. one gene has multiple transcripts), then Cufflinks does some sort of deconvolution to best determine which transcript a read belongs to.